scholarly journals Genome-Wide SNPs Redefines Species Boundaries and Conservation Units in the Freshwater Mussel Genus Cyprogenia of North America

2021 ◽  
Author(s):  
Kevin Roe ◽  
Kyung Seok Kim
Keyword(s):  
Phylogenetic Analyses ◽  
Freshwater Mussel ◽  
Conservation Units ◽  
Genetic Structuring ◽  
The North ◽  
Distinct Evolutionary Lineage ◽  
Snp Data ◽  
Genome Wide ◽  
Significant Difference ◽  
Tree Inference

Abstract Detailed information on species delineation and population genetic structure is a prerequisite for designing effective restoration and conservation strategies for imperiled organisms. Phylogenomic and population genomic analyses based on genome-wide ddRAD-Seq data has identified three allopatric lineages in the North American freshwater mussel genus Cyprogenia. Cyprogenia stegaria is restricted to the Eastern Highlands and displays little genetic structuring within this region. However, two allopatric clusters of C. aberti in the Ozark and Ouachita highlands exhibit substantial levels (mean FST = 0.120) of genetic differentiation and each warrants recognition as a distinct evolutionary lineage. Lineages of Cyprogenia in the Ouachita and Ozark highlands are further subdivided reflecting structuring at the level of river systems. Species tree inference and species delimitation in a Bayesian framework using SNP data supported results from phylogenetic analyses, which favors recognizing three species of Cyprogenia over the currently recognized two species.A comparison of SNPs generated from both destructively and non-destructively collected samples revealed no significant difference in the SNP error rate, quality and amount of ddRAD sequence reads, indicating that nondestructive or trace samples can be effectively utilized to generate SNP data for organisms for which destructive sampling is not permitted.

scholarly journals Genome-wide SNPs redefines species boundaries and conservation units in the freshwater mussel genus Cyprogenia of North America

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Kyung Seok Kim ◽  
Kevin J. Roe
Keyword(s):  
Phylogenetic Analyses ◽  
Freshwater Mussel ◽  
Conservation Strategies ◽  
Nucleotide Polymorphisms ◽  
Conservation Units ◽  
Genetic Structuring ◽  
The North ◽  
Snp Data ◽  
Genome Wide ◽  
Significant Difference

AbstractDetailed information on species delineation and population genetic structure is a prerequisite for designing effective restoration and conservation strategies for imperiled organisms. Phylogenomic and population genomic analyses based on genome-wide double digest restriction-site associated DNA sequencing (ddRAD-Seq) data has identified three allopatric lineages in the North American freshwater mussel genus Cyprogenia. Cyprogenia stegaria is restricted to the Eastern Highlands and displays little genetic structuring within this region. However, two allopatric lineages of C. aberti in the Ozark and Ouachita highlands exhibit substantial levels (mean uncorrected FST = 0.368) of genetic differentiation and each warrants recognition as a distinct evolutionary lineage. Lineages of Cyprogenia in the Ouachita and Ozark highlands are further subdivided reflecting structuring at the level of river systems. Species tree inference and species delimitation in a Bayesian framework using single nucleotide polymorphisms (SNP) data supported results from phylogenetic analyses, and supports three species of Cyprogenia over the currently recognized two species. A comparison of SNPs generated from both destructively and non-destructively collected samples revealed no significant difference in the SNP error rate, quality and amount of ddRAD sequence reads, indicating that nondestructive or trace samples can be effectively utilized to generate SNP data for organisms for which destructive sampling is not permitted.

scholarly journals Genome-wide sequence-based genotyping supports a nonhybrid origin of Castanea alabamensis

2019 ◽  
Author(s):  
M. Taylor Perkins ◽  
Tetyana Zhebentyayeva ◽  
Paul H. Sisco ◽  
J. Hill Craddock
Keyword(s):  
North American ◽  
Distinct Group ◽  
Morphological Diversity ◽  
Hybrid Origin ◽  
Putative Hybrid ◽  
Eastern United States ◽  
The North ◽  
Snp Data ◽  
Genome Wide ◽  
Conservation Concern

AbstractThe genus Castanea in North America contains multiple tree and shrub taxa of conservation concern. The two species within the group, American chestnut (Castanea dentata) and chinquapin (C. pumila sensu lato), display remarkable morphological diversity across their distributions in the eastern United States and southern Ontario. Previous investigators have hypothesized that hybridization between C. dentata and C. pumila has played an important role in generating morphological variation in wild populations. A putative hybrid taxon, Castanea alabamensis, was identified in northern Alabama in the early 20th century; however, the question of its hybridity has been unresolved. We tested the hypothesized hybrid origin of C. alabamensis using genome-wide sequence-based genotyping of C. alabamensis, all currently recognized North American Castanea taxa, and two Asian Castanea species at >100,000 single-nucleotide polymorphism (SNP) loci. With these data, we generated a high-resolution phylogeny, tested for admixture among taxa, and analyzed population genetic structure of the study taxa. Bayesian clustering and principal components analysis provided no evidence of admixture between C. dentata and C. pumila in C. alabamensis genomes. Phylogenetic analysis of genome-wide SNP data indicated that C. alabamensis forms a distinct group within C. pumila sensu lato. Our results are consistent with the model of a nonhybrid origin for C. alabamensis. Our finding of C. alabamensis as a genetically and morphologically distinct group within the North American chinquapin complex provides further impetus for the study and conservation of the North American Castanea species.

Regional population structuring and conservation units in the platypus (Ornithorhynchus anatinus)

2013 ◽  
Vol 61 (5) ◽  
pp. 378 ◽  
Author(s):  
Stephen H. Kolomyjec ◽  
Tom R. Grant ◽  
Christopher N. Johnson ◽  
David Blair
Keyword(s):  
Gene Flow ◽  
Genetic Differentiation ◽  
Large Scale ◽  
Wide Distribution ◽  
Conservation Units ◽  
Genetic Structuring ◽  
The North ◽  
Contemporary Gene Flow ◽  
Ornithorhynchus Anatinus ◽  
Southern Island

The platypus (Ornithorhynchus anatinus) has a wide distribution in Australia, encompassing the southern island of Tasmania and a broad latitudinal range of the mainland from the temperate south to the tropical north. We used 12 microsatellite markers from 235 individuals sampled from 13 river systems to examine patterns of genetic differentiation and gene flow throughout the species’ range. Using a Bayesian approach we identified three large-scale groupings that correspond closely to geographically distinct regions of the species’ distribution: the tropical northern mainland, the subtropical and temperate southern mainland, and Tasmania. Six additional clusters were found within the regional groups, three in the northern, two in the southern mainland regions, and the last in Tasmania. These clusters coincided with major river drainages. Genetic differentiation was generally high, with pairwise Fst values ranging from 0.065 to 0.368 for regions and 0.037 to 0.479 for clusters. We found no evidence of contemporary gene flow among the three clusters in the north, but some migration may occur between the larger clusters in the south. Due to the high genetic structuring and lack of gene flow between these three regional populations of the platypus we recommend their treatment as evolutionarily significant units (ESUs) within the platypus species. We have also detailed several smaller management units (MUs) existing within our study area based on subregional clusters and geographically significant features.

scholarly journals The genetic prehistory of the Greater Caucasus

2018 ◽  
Author(s):  
Chuan-Chao Wang ◽  
Sabine Reinhold ◽  
Alexey Kalmykov ◽  
Antje Wissgott ◽  
Guido Brandt ◽  
...  
Keyword(s):  
Native American ◽  
Human Movement ◽  
North Caucasus ◽  
Hunter Gatherers ◽  
The Caucasus ◽  
The North ◽  
European Languages ◽  
Snp Data ◽  
Genome Wide ◽  
Show Evidence

AbstractArchaeogenetic studies have described the formation of Eurasian ‘steppe ancestry’ as a mixture of Eastern and Caucasus hunter-gatherers. However, it remains unclear when and where this ancestry arose and whether it was related to a horizon of cultural innovations in the 4thmillennium BCE that subsequently facilitated the advance of pastoral societies likely linked to the dispersal of Indo-European languages. To address this, we generated genome-wide SNP data from 45 prehistoric individuals along a 3000-year temporal transect in the North Caucasus. We observe a genetic separation between the groups of the Caucasus and those of the adjacent steppe. The Caucasus groups are genetically similar to contemporaneous populations south of it, suggesting that – unlike today – the Caucasus acted as a bridge rather than an insurmountable barrier to human movement. The steppe groups from Yamnaya and subsequent pastoralist cultures show evidence for previously undetected farmer-related ancestry from different contact zones, while Steppe Maykop individuals harbour additional Upper Palaeolithic Siberian and Native American related ancestry.

scholarly journals Genome-Wide Sequence-Based Genotyping Supports a Nonhybrid Origin of Castanea alabamensis

2021 ◽  
Vol 46 (4) ◽  
pp. 973-984
Author(s):  
M. Taylor Perkins ◽  
Tetyana Zhebentyayeva ◽  
Paul H. Sisco ◽  
J. Hill Craddock
Keyword(s):  
North American ◽  
Distinct Group ◽  
Morphological Diversity ◽  
Hybrid Origin ◽  
Putative Hybrid ◽  
Eastern United States ◽  
The North ◽  
Snp Data ◽  
Genome Wide ◽  
Conservation Concern

Abstract— The genus Castanea in North America contains several tree and shrub taxa of conservation concern. The two species within the group, American chestnut (Castanea dentata) and chinquapin (C. pumila sensu lato), display remarkable morphological diversity across their distributions in the eastern United States and southern Ontario. Previous investigators have hypothesized that hybridization between C. dentata and C. pumila has played an important role in generating morphological variation in wild populations. A putative hybrid taxon, Castanea alabamensis, was identified in northern Alabama in the early 20th century; however, the question of its hybridity has been unresolved. We tested the hypothesized hybrid origin of C. alabamensis using genome-wide sequence-based genotyping of C. alabamensis, all currently recognized North American Castanea taxa, and two Asian Castanea species at > 100,000 single-nucleotide polymorphism (SNP) loci. With these data, we generated a high-resolution phylogeny, tested for admixture among taxa, and analyzed population genetic structure of the study taxa. Bayesian clustering and principal components analysis provided no evidence of admixture between C. dentata and C. pumila in C. alabamensis genomes. Phylogenetic analysis of genome-wide SNP data indicated that C. alabamensis forms a distinct group within C. pumila sensu lato. Our results are consistent with the model of a nonhybrid origin for C. alabamensis. Our finding of C. alabamensis as a genetically and morphologically distinct group within the North American chinquapin complex provides further impetus for the study and conservation of the North American Castanea species.

Conservation genetics of the wood turtle (Glyptemys insculpta) in Quebec, Canada

2005 ◽  
Vol 83 (6) ◽  
pp. 765-772 ◽  
Author(s):  
Nathalie Tessier ◽  
Sébastien Rioux Paquette ◽  
François-Joseph Lapointe
Keyword(s):  
Phylogenetic Analyses ◽  
Population Declines ◽  
Conservation Units ◽  
The North ◽  
Glyptemys Insculpta ◽  
South Shore ◽  
Two Populations ◽  
St Lawrence River ◽  
Wood Turtle

Throughout its range, the long-term persistence of the wood turtle (Glyptemys insculpta Le Conte, 1830) is jeopardized by habitat perturbations and commercial collection. The main objective of this study was to acquire knowledge on the genetic structure of wood turtle populations within Quebec, where the species reaches the northernmost limit of its range, to identify proper conservation units. The six known populations in Quebec were genetically characterized using five microsatellite loci. Genetic analyses revealed high variability among all populations (HO ranging from 0.561 to 0.886), suggesting that past population declines have not yet affected their genetic diversity. Since populations are located on both shores of the St. Lawrence River, two colonization hypotheses were tested to determine whether the River acted as a dispersal route or as a barrier. Results of AMOVA tests, phylogenetic analyses, and assignment tests demonstrated the clear distinction between populations from both shores, and three genetically different units were identified: the two populations on the north shore and a single homogenous group on the south shore.

RENDIMENTO DE CULTIVARES DE CAUPI (Vigna unguiculata L Walp.) SUBMETIDAS À DIFERENTES LÂMINAS DE IRRIGAÇÃO

Irriga ◽  
1999 ◽  
Vol 4 (3) ◽  
pp. 139-144 ◽  
Author(s):  
Gianini Peixoto Bezerra Lima ◽  
José Vanglesio de Aguiar ◽  
Raimundo Nonato Távora Costa ◽  
Vital Pedro da Silva Paz
Keyword(s):  
Vigna Unguiculata ◽  
Irrigation System ◽  
Northeast Brazil ◽  
Marginal Product ◽  
Applied Water ◽  
Cowpea Cultivars ◽  
The North ◽  
Significant Difference ◽  
Caixa Postal ◽  
Water Depths

RENDIMENTO DE CULTIVARES DE CAUPI (Vigna unguiculata L Walp.) SUBMETIDAS À DIFERENTES LÂMINAS DE IRRIGAÇÃO1       Gianini Peixoto Bezerra Lima José Vanglesio de Aguiar Raimundo Nonato Távora Costa Universidade Federal do Ceará – Departamento de Engenharia Agrícola. Campus do Pici. Bloco 804. CEP 60455-760 – Fortaleza-CE Vital Pedro da Silva Paz Escola Superior de Agricultura Luiz de Queiroz – Departamento de Engenharia Rural, bolsista da FAPESP. Av. Pádua Dias, 11 – Caixa Postal 11. 13418-900 – Piracicaba-SP       1 RESUMO       O caupi é um dos cultivos mais tradicionais do Norte e Nordeste do Brasil, constituindo alimento básico nestas regiões. Com este trabalho foi possível estabelecer relações entre a quantidade de água aplicada e produtividade de grãos, para três variedades de feijão caupi submetidas a diferentes lâminas de água. Para caracterização das lâminas de água foi utilizado um sistema de irrigação por aspersão convencional em linha. O controle da irrigação foi realizado a partir de tensiômetros instalados à 15 cm de profundidade. Os resultados mostraram que: i) a cultivar João Paulo II apresentou melhores resultados de produtividade para as lâminas de água aplicadas que variaram de T1 = 291,8 mm a T5 = 141,2 mm; ii) sob condições de reduzida disponibilidade de água, ou seja, menor lâmina aplicada, não ocorreu diferença estatística  para a produtividade entre as cultivares estudadas; e iii) para as condições do estudo, a cultivar Setentão apresentou a menor taxa de redução do produto marginal.       UNITERMOS: caupi, irrigação, função de produção       LIMA, G. P. B., AGUIAR, J. V., COSTA, R. N. T., PAZ, V. P. S. Responses OF cowpea cultivars (Vigna unguiculata L Walp) at differents irrigation deficits     2 ABSTRACT       The caupi is one of the most traditional cultivation of the north and northeast - Brazil, constituting a basic food in these areas. With this work it was possible to establish relationships between the amount of water applied and productivity of grains, for three caupi varieties submitted to different irrigation sheets. To diferentiate water depths in the irrigation system, the aspersion in line was used. The control of the irrigation was accomplished using tensiometers installed to 15 cm of depth. The results showed that: i) the João Paulo II variety presented better productivity for the applied water depths; ii) under reduced conditions of water avai lability for study conditions, these was no significant difference in the productivity reached among the cultivars studied; and iii) for the conditions of the study, the variety Setentão presented the smallest rate of reduction of the marginal product.       KEYWORDS: cowpea, irrigation, production function  

Diversification of the North American Doellingeria-Eucephalus Clade (Astereae: Asteraceae) Inferred from Molecular and Morphological Evidence

2019 ◽  
Vol 44 (4) ◽  
pp. 930-942
Author(s):  
Geraldine A. Allen ◽  
Luc Brouillet ◽  
John C. Semple ◽  
Heidi J. Guest ◽  
Robert Underhill
Keyword(s):  
North American ◽  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Sister Group ◽  
Morphological Evidence ◽  
South American ◽  
New Combinations ◽  
The North ◽  
Hybridization Event ◽  
Ancient Hybridization

Abstract—Doellingeria and Eucephalus form the earliest-diverging clade of the North American Astereae lineage. Phylogenetic analyses of both nuclear and plastid sequence data show that the Doellingeria-Eucephalus clade consists of two main subclades that differ from current circumscriptions of the two genera. Doellingeria is the sister group to E. elegans, and the Doellingeria + E. elegans subclade in turn is sister to the subclade containing all remaining species of Eucephalus. In the plastid phylogeny, the two subclades are deeply divergent, a pattern that is consistent with an ancient hybridization event involving ancestral species of the Doellingeria-Eucephalus clade and an ancestral taxon of a related North American or South American group. Divergence of the two Doellingeria-Eucephalus subclades may have occurred in association with northward migration from South American ancestors. We combine these two genera under the older of the two names, Doellingeria, and propose 12 new combinations (10 species and two varieties) for all species of Eucephalus.

Association between hTERT Polymorphisms and Female Papillary Thyroid Carcinoma

2019 ◽  
Vol 14 (3) ◽  
pp. 268-279
Author(s):  
Ying Liu ◽  
Zhi Li ◽  
Xinyue Tang ◽  
Min Li ◽  
Feng Shi
Keyword(s):  
Papillary Thyroid Carcinoma ◽  
Thyroid Carcinoma ◽  
Genome Wide Association Study ◽  
Papillary Thyroid ◽  
Clinicopathologic Characteristics ◽  
Female Population ◽  
Genome Wide ◽  
Increased Risk ◽  
Significant Difference ◽  
Thyroid Cancer Risk

Background: A previous genome-wide association study showed that hTERT rs10069690 and rs2736100 polymorphisms were associated with thyroid cancer risk. Objective: This study further investigated the association between increased risk and clinicopathologic characteristics for Papillary Thyroid Carcinoma (PTC) and hTERT polymorphisms rs10069690 or rs2736100 in a Chinese female population. Methods: The hTERT genotypes of 276 PTC patients and 345 healthy subjects were determined with regard to SNPs rs10069690 and rs2736100. The association between these SNPs and the risk of PTC and clinicopathologic characteristics was investigated by logistic regression. Results: We found a significant difference between PTC and rs10069690 (Odds Ratio (OR) = 1.515; P = 0.005), but not between PTC and rs2736100. When the analysis was limited to females, rs10069690 and rs2736100 were both associated with increased risk for PTC in female individuals (OR = 1.647, P = 0.007; OR = 1.339, P = 0.041, respectively). Further haplotype analysis revealed a stimulative effect of haplotypes TC and CA of TERT rs10069690-rs2736100, which increased risk for PTC in female individuals (OR = 1.579, P = 0.014; OR = 0.726, P = 0.025, respectively). Furthermore, the heterozygote A/C of rs2736100 showed significant difference for age (OR = 0.514, P = 0.047). Conclusion: Our finding suggests that hTERT polymorphisms rs10069690 and rs2736100 are associated with increased risk for PTC in Chinese female population and rs2736100 may be related to age. Consistent with US20170360914 and US20170232075, they are expected to be a potential molecular target for anti-cancer therapy.

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